Water hammer can take several different forms - either a load banb when a tap or valve is turned off, a vibration in the pipe work or high pitched wine. There are various causes for this such as high water pressure, badly installed pipework or wear/scale build up in taps and valves. As you do not state what sort of a noise is being made, I am guesing the float valve in the cisters either has some wear or scale build up, as in my experience is the most common problem. I would suggest changing this valve in the first instance and see if that solves the problem.
Your second point is the water rising when you flush the toilet. This does suggest a restriction some where in the soil pipe which should be investigated before it becomes a major problem. I would suggest you find the manhole where the toilet runs to, and use a set of drain rods to check for obstructions.
Hope this helps
John, May 2008